Rocket launchers have their magazines on the right side of the weapon. However, in the ending cutscene the magazine is on the left side.
In Doom 3, Mr. Bertruger's right eye is blind. In Doom 3: Resurrection of Evil, his left eye is blind.
Bertruger's blind eye is on the opposite side of his face from Doom 3.
The BFG 9000 ammunition pickup is square, but the cell is round.
Mars' gravity is only 45% as strong as Earth's gravity, yet the Marine when outside of com-pressurized buildings walking on Mars's surface, is still walking on the ground as if there is no difference in strength of gravity.
The biometric information on each PDA is identical in spite of belonging to different people.
The suits worn by all characters are short sleeved, which would make them incapable of protecting the operator in a low-oxygen atmosphere.
Some zombies are headless, yet when hey are gibbed the gibs contain a brain.
Weapons eject shells from the left side of the weapon. Weapons are usually designed to eject shells from the right side of the weapon and away from the firer's face.
If the hull of the base gets compromised, there is no blast of outgoing air from either the hole or the door leading back to a pressurized area.
It is not explained how flies could have made the journey from Earth.
The Player is tasked with shutting down a reactor, even though the reason he is doing this is to get more power.